Variant simulator; report

Node used for reconstructing ancestral genome sequence

If a (newick) phylogenetic tree file has been provided, the visualisation of the MSA used in the calculations is shown below. The two chosen groups (i.e. ‘ingroup’ / species of interest, and outgroup) are highlighted in the tree. The outgroup, used in the computation or not, is the outgroup, which together with the reference species of interest coalesce at the node of interest, from which the ancestral sequence have been extracted. Most recent common ancestor (MRCA) is highlighted in purple and labeled. The rest of the clades in the alignment are shown in lighter grey. Regardless whether a reconstructed ancestral sequence at a node, or an outgroup, has been chosen as the ancestor, the MRCA will be highlighted.

Distribution of simulated variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of simulated variants is shown across the genome of the species of interest. The grey distribution corresponds to the total amount of simulated variants, whereas the red distribution corresponds to the subset that is overlapping with a corresponding non-gap ancestral sequence. If there is no forced sub-sampling due to lack of ancestral sequence, the distribution will be fully red.

Distribution of derived variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of derived variants is shown across the genome of the species of interest. The distribution of derived variants across the genome is shown in red.

How much of the reference genome that has an available, aligned reconstructed ancestral sequence

Table 1 Fraction of refence genome that has an available aligned reconstructed ancestral sequence. The leftmost column represents the total size of the source chromosome (in base pairs), from the species of interest. The middle column represents the size (in base pairs) of the recontructed ancestral genome (or size of aligned outgroup without gaps). The rightmost column represents the fraction of the reference genome that is covered by an ancestral sequence, i.e. the fraction of the reference with a corresponding non-gap ancestral alignment.
Size of ref. genome Size of reconstructed genome Fraction covered of ref. genome
1 274 330 532 77 958 442 0.28
2 151 935 994 37 987 275 0.25
3 132 848 913 36 075 051 0.27
4 130 910 915 32 274 536 0.25
5 104 526 007 25 907 583 0.25
6 170 843 587 47 162 525 0.28
7 121 844 099 32 858 558 0.27
8 138 966 237 37 904 275 0.27
9 139 512 083 36 146 178 0.26
10 69 359 453 17 065 690 0.25
11 79 169 978 18 718 223 0.24
12 61 602 749 15 604 813 0.25
13 208 334 590 53 478 776 0.26
14 141 755 446 35 780 783 0.25
15 140 412 725 39 746 541 0.28
16 79 944 280 23 896 868 0.30
17 63 494 081 7 663 816 0.12
18 55 982 971 16 121 137 0.29
X 125 939 595 20 680 709 0.16

Number of simulated variants

and how many are overlapping with an available ancestral sequence

Table with corresponding data:
Table 2.
Fraction of simulated SNPs that is overlapping with a reconstructed ancestral sequence. Column explanation from left to right:
i) chromosome number
ii) the total number of simulated SNPs
iii) the number of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
iv) the fraction of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
v) the total number of derived variants.
No of sim. SNPs Number of sim. SNPs overlapping ancestral seq. Fraction of sim. SNPs overlapping ancestral seq. Number of derived variants
1 19 765 579 5 619 130 0.28 5 711 181
2 10 686 500 2 690 329 0.25 2 902 855
3 10 826 734 2 950 754 0.27 2 836 785
4 9 233 401 2 294 649 0.25 2 461 714
5 7 225 082 1 748 983 0.24 1 925 212
6 13 675 953 3 769 846 0.28 3 625 578
7 9 085 744 2 433 730 0.27 2 454 095
8 10 455 019 2 872 672 0.27 2 913 995
9 10 141 986 2 627 113 0.26 2 780 258
10 5 609 894 1 380 983 0.25 1 414 486
11 5 792 293 1 383 048 0.24 1 492 776
12 5 084 866 1 296 574 0.25 1 240 632
13 13 282 043 3 409 273 0.26 3 858 113
14 9 907 172 2 502 715 0.25 2 686 341
15 9 908 334 2 792 934 0.28 2 870 751
16 6 457 212 1 941 028 0.30 1 843 426
17 3 128 391 379 779 0.12 618 629
18 4 827 969 1 399 080 0.29 1 285 315
X 5 646 989 952 805 0.17 1 450 650

Types of simulated mutations

Table with corresponding data:
Table 3
Fraction of mutation types across the simulated variants with an available corresponding ancestral sequence. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions
v) the fraction of CpG site mutations
vi) the fraction of non-CpG mutations (transitions + transversions)
No. of SNPs Fraction transitions Fraction transversions Fraction CpGs Fraction non-CpGs (1-CpGs)
1 5 619 130 0.50 0.33 0.17 0.83
2 2 690 329 0.47 0.31 0.22 0.78
3 2 950 754 0.46 0.30 0.24 0.76
4 2 294 649 0.47 0.31 0.22 0.78
5 1 748 983 0.48 0.31 0.21 0.79
6 3 769 846 0.47 0.30 0.24 0.76
7 2 433 730 0.48 0.31 0.22 0.78
8 2 872 672 0.50 0.32 0.18 0.82
9 2 627 113 0.49 0.32 0.19 0.81
10 1 380 983 0.47 0.30 0.23 0.77
11 1 383 048 0.47 0.30 0.23 0.77
12 1 296 574 0.43 0.27 0.30 0.70
13 3 409 273 0.50 0.33 0.17 0.83
14 2 502 715 0.47 0.30 0.22 0.78
15 2 792 934 0.51 0.33 0.16 0.84
16 1 941 028 0.50 0.33 0.17 0.83
17 379 779 0.36 0.23 0.42 0.58
18 1 399 080 0.47 0.30 0.22 0.78
X 952 805 0.44 0.28 0.28 0.72

Types of derived mutations*

  • CpG mutation information is not available.

##### Table with corresponding data:

Table 4
Fraction of mutation types across the derived variants. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions.
No. of SNPs Fraction transitions Fraction transversions
1 5 711 181 0.62 0.38
2 2 902 855 0.61 0.39
3 2 836 785 0.60 0.40
4 2 461 714 0.61 0.39
5 1 925 212 0.61 0.39
6 3 625 578 0.61 0.39
7 2 454 095 0.61 0.39
8 2 913 995 0.60 0.40
9 2 780 258 0.61 0.39
10 1 414 486 0.59 0.41
11 1 492 776 0.59 0.41
12 1 240 632 0.60 0.40
13 3 858 113 0.62 0.38
14 2 686 341 0.61 0.39
15 2 870 751 0.62 0.38
16 1 843 426 0.61 0.39
17 618 629 0.60 0.40
18 1 285 315 0.60 0.40
X 1 450 650 0.60 0.40

Visualisation of gene density

and CDS overlap

Validation of simulation parameters

Number of mutations, fractions, and substitution rates. To make sure the simulation was performed as expected, the leftmost part is the calculated numbers and rates in the parameter files, including the total number of simulated variants per chromosome, based on information from the ancestor and reference species. The middle part is the (re)calculated numbers and rates based on the total number of simulated variants. The rightmost part is the (re)calculated numbers and rates within the subset with a corresponding non-gap ancestral sequence. The comparison of parameters and simulated variants is to make sure that the simulation has been perform as intended, and the comparison between total set and the subset is to make sure that the distribution is the same even if the variants are forced to be down-sampled due to the lack of an available ancestral sequence.

Comparison of numebr of mutations between log files and actual simulated files
Parameter files
Simulated variant file
Simulated variant file
(filtered for positions with a corresponding non-gap ancestral position)
Chromosome considered: 1 Chromosome considered: 1 Chromosome considered: 1
Total mut: 7170871 Total mut: 16491811 Total mut: 4680942
#AC AG AT #AC AG AT #AC AG AT
505899 1203850 426765 1276181 2846251 912695 361871 804297 258248
7.05% 16.79% 5.95% 7.74% 17.26% 5.53% 7.73% 17.18% 5.52%
#CA CG CT #CA CG CT #CA CG CT
248150 210751 989195 531840 526327 2144321 152110 150278 611577
3.46% 2.94% 13.79% 3.22% 3.19% 13.00% 3.25% 3.21% 13.07%
#GA GC GT #GA GC GT #GA GC GT
990615 212456 249134 2144933 529050 530830 610382 150858 151422
13.81% 2.96% 3.47% 13.01% 3.21% 3.22% 13.04% 3.22% 3.23%
#TA TC TG #TA TC TG #TA TC TG
425499 1204034 504523 914575 2853705 1281103 259172 808053 362674
5.93% 16.79% 7.04% 5.55% 17.30% 7.77% 5.54% 17.26% 7.75%
Total CpG mut: 951402 Total CpG mut: 3273768 Total CpG mut: 938188
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
85904 74336 315175 285810 287296 1063586 81896 82193 305085
9.03% 7.81% 33.13% 8.73% 8.78% 32.49% 8.73% 8.76% 32.52%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
315902 74029 86056 1062812 288056 286208 304060 82594 82360
33.20% 7.78% 9.05% 32.46% 8.80% 8.74% 32.41% 8.80% 8.78%
Chromosome considered: 2 Chromosome considered: 2 Chromosome considered: 2
Total mut: 3672736 Total mut: 24877378 Total mut: 6779147
#AC AG AT #AC AG AT #AC AG AT
290738 635901 202103 1903416 4245389 1362572 518953 1156129 370870
7.92% 17.31% 5.50% 7.65% 17.07% 5.48% 7.66% 17.05% 5.47%
#CA CG CT #CA CG CT #CA CG CT
115062 120830 471057 815280 807450 3292306 222942 220328 897434
3.13% 3.29% 12.83% 3.28% 3.25% 13.23% 3.29% 3.25% 13.24%
#GA GC GT #GA GC GT #GA GC GT
472120 121319 114935 3291693 811040 816195 896084 220431 222756
12.85% 3.30% 3.13% 13.23% 3.26% 3.28% 13.22% 3.25% 3.29%
#TA TC TG #TA TC TG #TA TC TG
202636 635705 290330 1364301 4258487 1909249 371824 1160551 520845
5.52% 17.31% 7.91% 5.48% 17.12% 7.67% 5.48% 17.12% 7.68%
Total CpG mut: 508507 Total CpG mut: 5574701 Total CpG mut: 1530312
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
43521 45666 165014 485821 489656 1812178 133499 134151 497871
8.56% 8.98% 32.45% 8.71% 8.78% 32.51% 8.72% 8.77% 32.53%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
165122 45358 43826 1809531 489667 487848 496065 134561 134165
32.47% 8.92% 8.62% 32.46% 8.78% 8.75% 32.42% 8.79% 8.77%
Chromosome considered: 3 Chromosome considered: 3 Chromosome considered: 3
Total mut: 3640054 Total mut: 33139779 Total mut: 9021935
#AC AG AT #AC AG AT #AC AG AT
309247 649572 192925 2508234 5591319 1793690 682582 1519603 487521
8.50% 17.85% 5.30% 7.57% 16.87% 5.41% 7.57% 16.84% 5.40%
#CA CG CT #CA CG CT #CA CG CT
106426 122725 439330 1105281 1095732 4461447 302292 299072 1216262
2.92% 3.37% 12.07% 3.34% 3.31% 13.46% 3.35% 3.31% 13.48%
#GA GC GT #GA GC GT #GA GC GT
438987 122942 107403 4462185 1098900 1106551 1214876 298901 301590
12.06% 3.38% 2.95% 13.46% 3.32% 3.34% 13.47% 3.31% 3.34%
#TA TC TG #TA TC TG #TA TC TG
192458 648129 309910 1795695 5606283 2514462 488510 1526165 684561
5.29% 17.81% 8.51% 5.42% 16.92% 7.59% 5.41% 16.92% 7.59%
Total CpG mut: 524541 Total CpG mut: 8139034 Total CpG mut: 2238278
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
43990 51599 166489 709262 715752 2644626 195171 196773 727322
8.39% 9.84% 31.74% 8.71% 8.79% 32.49% 8.72% 8.79% 32.49%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
166821 51850 43792 2642339 715147 711908 725672 196883 196457
31.80% 9.88% 8.35% 32.47% 8.79% 8.75% 32.42% 8.80% 8.78%
Chromosome considered: 4 Chromosome considered: 4 Chromosome considered: 4
Total mut: 3186288 Total mut: 40417423 Total mut: 10816061
#AC AG AT #AC AG AT #AC AG AT
263128 580420 177058 3061612 6823791 2188610 818492 1822016 584529
8.26% 18.22% 5.56% 7.57% 16.88% 5.42% 7.57% 16.85% 5.40%
#CA CG CT #CA CG CT #CA CG CT
92614 97193 380373 1346222 1335505 5436427 361840 358425 1457541
2.91% 3.05% 11.94% 3.33% 3.30% 13.45% 3.35% 3.31% 13.48%
#GA GC GT #GA GC GT #GA GC GT
382430 97956 94514 5438780 1338887 1349275 1457332 358645 361508
12.00% 3.07% 2.97% 13.46% 3.31% 3.34% 13.47% 3.32% 3.34%
#TA TC TG #TA TC TG #TA TC TG
177049 579398 264155 2190818 6839713 3067783 585380 1829549 820804
5.56% 18.18% 8.29% 5.42% 16.92% 7.59% 5.41% 16.92% 7.59%
Total CpG mut: 377378 Total CpG mut: 10094791 Total CpG mut: 2738801
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
32870 34198 121067 880533 887388 3279398 239241 240595 889546
8.71% 9.06% 32.08% 8.72% 8.79% 32.49% 8.74% 8.78% 32.48%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
121011 34799 33433 3277335 886865 883272 888147 240949 240323
32.07% 9.22% 8.86% 32.47% 8.79% 8.75% 32.43% 8.80% 8.77%
Chromosome considered: 5 Chromosome considered: 5 Chromosome considered: 5
Total mut: 2443703 Total mut: 45980913 Total mut: 12200087
#AC AG AT #AC AG AT #AC AG AT
196998 435724 137103 3480603 7758578 2488681 923711 2056708 660041
8.06% 17.83% 5.61% 7.57% 16.87% 5.41% 7.57% 16.86% 5.41%
#CA CG CT #CA CG CT #CA CG CT
73508 73539 303828 1532794 1521566 6191481 407321 403643 1640588
3.01% 3.01% 12.43% 3.33% 3.31% 13.47% 3.34% 3.31% 13.45%
#GA GC GT #GA GC GT #GA GC GT
305103 73532 73572 6195726 1525071 1536270 1641705 403554 407219
12.49% 3.01% 3.01% 13.47% 3.32% 3.34% 13.46% 3.31% 3.34%
#TA TC TG #TA TC TG #TA TC TG
136769 436580 197447 2489289 7773733 3487121 661185 2067224 927188
5.60% 17.87% 8.08% 5.41% 16.91% 7.58% 5.42% 16.94% 7.60%
Total CpG mut: 287014 Total CpG mut: 11756383 Total CpG mut: 3103758
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
25244 25034 92686 1025606 1033699 3818641 271095 273039 1007736
8.80% 8.72% 32.29% 8.72% 8.79% 32.48% 8.73% 8.80% 32.47%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
93829 24955 25266 3817370 1032674 1028393 1006809 272883 272196
32.69% 8.69% 8.80% 32.47% 8.78% 8.75% 32.44% 8.79% 8.77%
Chromosome considered: 6 Chromosome considered: 6 Chromosome considered: 6
Total mut: 4607080 Total mut: 56421446 Total mut: 15080977
#AC AG AT #AC AG AT #AC AG AT
383652 824985 239690 4237532 9445348 3029668 1133204 2523578 810414
8.33% 17.91% 5.20% 7.51% 16.74% 5.37% 7.51% 16.73% 5.37%
#CA CG CT #CA CG CT #CA CG CT
134721 156281 564874 1903566 1889660 7690502 509389 504839 2053995
2.92% 3.39% 12.26% 3.37% 3.35% 13.63% 3.38% 3.35% 13.62%
#GA GC GT #GA GC GT #GA GC GT
562941 156657 134239 7690880 1893562 1909052 2053049 504485 509772
12.22% 3.40% 2.91% 13.63% 3.36% 3.38% 13.61% 3.35% 3.38%
#TA TC TG #TA TC TG #TA TC TG
240700 825162 383178 3029956 9457379 4244341 809881 2531550 1136821
5.22% 17.91% 8.32% 5.37% 16.76% 7.52% 5.37% 16.79% 7.54%
Total CpG mut: 666984 Total CpG mut: 14991803 Total CpG mut: 3992714
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
55122 63962 213992 1307795 1318223 4869472 348357 351452 1296407
8.26% 9.59% 32.08% 8.72% 8.79% 32.48% 8.72% 8.80% 32.47%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
214706 64532 54670 4868551 1316662 1311100 1295943 351074 349481
32.19% 9.68% 8.20% 32.47% 8.78% 8.75% 32.46% 8.79% 8.75%
Chromosome considered: 7 Chromosome considered: 7 Chromosome considered: 7
Total mut: 3103273 Total mut: 63492497 Total mut: 16990408
#AC AG AT #AC AG AT #AC AG AT
247975 542702 170984 4763448 10616902 3403016 1275863 2840710 911543
7.99% 17.49% 5.51% 7.50% 16.72% 5.36% 7.51% 16.72% 5.37%
#CA CG CT #CA CG CT #CA CG CT
94669 97198 398021 2146333 2129511 8669907 574682 569581 2317170
3.05% 3.13% 12.83% 3.38% 3.35% 13.66% 3.38% 3.35% 13.64%
#GA GC GT #GA GC GT #GA GC GT
400016 97976 95490 8672686 2135925 2152875 2316060 569207 575173
12.89% 3.16% 3.08% 13.66% 3.36% 3.39% 13.63% 3.35% 3.39%
#TA TC TG #TA TC TG #TA TC TG
170534 540073 247635 3406180 10625932 4769782 911799 2849674 1278946
5.50% 17.40% 7.98% 5.36% 16.74% 7.51% 5.37% 16.77% 7.53%
Total CpG mut: 427984 Total CpG mut: 17006496 Total CpG mut: 4517013
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
36089 37083 140081 1484317 1495181 5523429 394367 397478 1466297
8.43% 8.66% 32.73% 8.73% 8.79% 32.48% 8.73% 8.80% 32.46%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
140835 37491 36405 5522902 1493955 1486712 1466396 397337 395138
32.91% 8.76% 8.51% 32.48% 8.78% 8.74% 32.46% 8.80% 8.75%
Chromosome considered: 8 Chromosome considered: 8 Chromosome considered: 8
Total mut: 3776009 Total mut: 72151819 Total mut: 19352642
#AC AG AT #AC AG AT #AC AG AT
305729 679134 223247 5440755 12129171 3887002 1460125 3251527 1043677
8.10% 17.99% 5.91% 7.54% 16.81% 5.39% 7.54% 16.80% 5.39%
#CA CG CT #CA CG CT #CA CG CT
115794 109857 455364 2420413 2401833 9776933 649898 644251 2620862
3.07% 2.91% 12.06% 3.35% 3.33% 13.55% 3.36% 3.33% 13.54%
#GA GC GT #GA GC GT #GA GC GT
454583 109258 115607 9778634 2408558 2427779 2618819 643767 650737
12.04% 2.89% 3.06% 13.55% 3.34% 3.36% 13.53% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
222552 679641 305243 3891633 12139248 5449860 1043949 3261454 1463576
5.89% 18.00% 8.08% 5.39% 16.82% 7.55% 5.39% 16.85% 7.56%
Total CpG mut: 407679 Total CpG mut: 18802193 Total CpG mut: 5027451
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
37300 35268 131075 1641903 1653120 6105517 439302 442519 1631377
9.15% 8.65% 32.15% 8.73% 8.79% 32.47% 8.74% 8.80% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
131503 35373 37160 6105671 1651781 1644201 1632610 441847 439796
32.26% 8.68% 9.12% 32.47% 8.79% 8.74% 32.47% 8.79% 8.75%
Chromosome considered: 9 Chromosome considered: 9 Chromosome considered: 9
Total mut: 3567644 Total mut: 80320188 Total mut: 21468040
#AC AG AT #AC AG AT #AC AG AT
284767 635521 200869 6063549 13516249 4331274 1620725 3611982 1158546
7.98% 17.81% 5.63% 7.55% 16.83% 5.39% 7.55% 16.82% 5.40%
#CA CG CT #CA CG CT #CA CG CT
107492 109814 446240 2689590 2668105 10864138 719591 713370 2902273
3.01% 3.08% 12.51% 3.35% 3.32% 13.53% 3.35% 3.32% 13.52%
#GA GC GT #GA GC GT #GA GC GT
446877 110495 108947 10866967 2677244 2698271 2901106 713179 720690
12.53% 3.10% 3.05% 13.53% 3.33% 3.36% 13.51% 3.32% 3.36%
#TA TC TG #TA TC TG #TA TC TG
199813 630881 285928 4338901 13531190 6074710 1159547 3621997 1625034
5.60% 17.68% 8.01% 5.40% 16.85% 7.56% 5.40% 16.87% 7.57%
Total CpG mut: 430091 Total CpG mut: 20775810 Total CpG mut: 5539166
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
37371 37488 140080 1814875 1826518 6745366 484191 487655 1796979
8.69% 8.72% 32.57% 8.74% 8.79% 32.47% 8.74% 8.80% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
140977 36788 37387 6746507 1825391 1817153 1799053 486485 484803
32.78% 8.55% 8.69% 32.47% 8.79% 8.75% 32.48% 8.78% 8.75%
Chromosome considered: 10 Chromosome considered: 10 Chromosome considered: 10
Total mut: 1899213 Total mut: 84634363 Total mut: 22530078
#AC AG AT #AC AG AT #AC AG AT
181966 361243 102110 6386472 14236665 4563273 1699993 3788810 1215672
9.58% 19.02% 5.38% 7.55% 16.82% 5.39% 7.55% 16.82% 5.40%
#CA CG CT #CA CG CT #CA CG CT
49033 60742 196522 2835571 2813035 11454891 755527 749229 3047185
2.58% 3.20% 10.35% 3.35% 3.32% 13.53% 3.35% 3.33% 13.52%
#GA GC GT #GA GC GT #GA GC GT
195926 60644 49339 11455594 2822358 2844659 3046091 749137 756885
10.32% 3.19% 2.60% 13.54% 3.33% 3.36% 13.52% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
101831 358374 181483 4570211 14252598 6399036 1216482 3799689 1705378
5.36% 18.87% 9.56% 5.40% 16.84% 7.56% 5.40% 16.86% 7.57%
Total CpG mut: 209423 Total CpG mut: 22071529 Total CpG mut: 5858111
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
17902 21404 65597 1928087 1940546 7165726 512273 515823 1900455
8.55% 10.22% 31.32% 8.74% 8.79% 32.47% 8.74% 8.81% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
64931 21545 18044 7167658 1938644 1930868 1902503 514240 512817
31.00% 10.29% 8.62% 32.47% 8.78% 8.75% 32.48% 8.78% 8.75%
Chromosome considered: 11 Chromosome considered: 11 Chromosome considered: 11
Total mut: 1972571 Total mut: 89133737 Total mut: 23595009
#AC AG AT #AC AG AT #AC AG AT
174199 368596 109370 6734802 15012487 4812334 1782047 3971393 1274204
8.83% 18.69% 5.54% 7.56% 16.84% 5.40% 7.55% 16.83% 5.40%
#CA CG CT #CA CG CT #CA CG CT
56549 60900 216125 2980604 2956727 12039076 790119 783435 3186947
2.87% 3.09% 10.96% 3.34% 3.32% 13.51% 3.35% 3.32% 13.51%
#GA GC GT #GA GC GT #GA GC GT
215726 60692 56248 12039497 2965957 2989398 3186042 783660 791372
10.94% 3.08% 2.85% 13.51% 3.33% 3.35% 13.50% 3.32% 3.35%
#TA TC TG #TA TC TG #TA TC TG
110742 368394 175030 4820086 15033232 6749537 1275037 3983216 1787537
5.61% 18.68% 8.87% 5.41% 16.87% 7.57% 5.40% 16.88% 7.58%
Total CpG mut: 214177 Total CpG mut: 23364448 Total CpG mut: 6176228
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
19167 20803 66906 2040685 2054515 7585755 539830 543857 2003833
8.95% 9.71% 31.24% 8.73% 8.79% 32.47% 8.74% 8.81% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
66913 20884 19504 7587718 2052418 2043357 2005822 542238 540648
31.24% 9.75% 9.11% 32.48% 8.78% 8.75% 32.48% 8.78% 8.75%
Chromosome considered: 12 Chromosome considered: 12 Chromosome considered: 12
Total mut: 1607400 Total mut: 92735053 Total mut: 24502303
#AC AG AT #AC AG AT #AC AG AT
150180 307166 75675 6985055 15567981 4990833 1844802 4110962 1318585
9.34% 19.11% 4.71% 7.53% 16.79% 5.38% 7.53% 16.78% 5.38%
#CA CG CT #CA CG CT #CA CG CT
40605 60874 170238 3115133 3090799 12582619 824496 817508 3324592
2.53% 3.79% 10.59% 3.36% 3.33% 13.57% 3.36% 3.34% 13.57%
#GA GC GT #GA GC GT #GA GC GT
171115 61234 40611 12584839 3100258 3124244 3324046 817746 825313
10.65% 3.81% 2.53% 13.57% 3.34% 3.37% 13.57% 3.34% 3.37%
#TA TC TG #TA TC TG #TA TC TG
75730 305055 148917 4999195 15592840 7001257 1320041 4123588 1850624
4.71% 18.98% 9.26% 5.39% 16.81% 7.55% 5.39% 16.83% 7.55%
Total CpG mut: 243951 Total CpG mut: 24847998 Total CpG mut: 6565508
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
19467 28049 74205 2170213 2185202 8067219 573994 578360 2129750
7.98% 11.50% 30.42% 8.73% 8.79% 32.47% 8.74% 8.81% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
74811 28183 19236 8069978 2182663 2172723 2132706 576337 574361
30.67% 11.55% 7.89% 32.48% 8.78% 8.74% 32.48% 8.78% 8.75%
Chromosome considered: 13 Chromosome considered: 13 Chromosome considered: 13
Total mut: 4777528 Total mut: 103737311 Total mut: 27327307
#AC AG AT #AC AG AT #AC AG AT
308486 772525 289471 7838691 17471719 5601367 2063717 4599508 1475323
6.46% 16.17% 6.06% 7.56% 16.84% 5.40% 7.55% 16.83% 5.40%
#CA CG CT #CA CG CT #CA CG CT
177431 138909 701665 3467354 3440080 14005578 915183 907540 3692168
3.71% 2.91% 14.69% 3.34% 3.32% 13.50% 3.35% 3.32% 13.51%
#GA GC GT #GA GC GT #GA GC GT
701296 139933 177233 14007127 3451226 3478120 3691477 908647 915973
14.68% 2.93% 3.71% 13.50% 3.33% 3.35% 13.51% 3.33% 3.35%
#TA TC TG #TA TC TG #TA TC TG
289835 772138 308606 5614577 17502230 7859242 1476944 4611412 2069415
6.07% 16.16% 6.46% 5.41% 16.87% 7.58% 5.40% 16.87% 7.57%
Total CpG mut: 657042 Total CpG mut: 27127783 Total CpG mut: 7149777
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
60058 47466 220569 2369666 2384831 8808051 625071 629546 2319596
9.14% 7.22% 33.57% 8.74% 8.79% 32.47% 8.74% 8.81% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
221423 47361 60165 8810395 2382704 2372136 2322776 627563 625225
33.70% 7.21% 9.16% 32.48% 8.78% 8.74% 32.49% 8.78% 8.74%
Chromosome considered: 14 Chromosome considered: 14 Chromosome considered: 14
Total mut: 3369919 Total mut: 111447671 Total mut: 29273663
#AC AG AT #AC AG AT #AC AG AT
257088 579335 185663 8407725 18740570 6007954 2207342 4920095 1578043
7.63% 17.19% 5.51% 7.54% 16.82% 5.39% 7.54% 16.81% 5.39%
#CA CG CT #CA CG CT #CA CG CT
107023 107181 447488 3733359 3703715 15080241 982140 974190 3963720
3.18% 3.18% 13.28% 3.35% 3.32% 13.53% 3.36% 3.33% 13.54%
#GA GC GT #GA GC GT #GA GC GT
448540 107595 107987 15082830 3715803 3744645 3962691 975273 982988
13.31% 3.19% 3.20% 13.53% 3.33% 3.36% 13.54% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
184778 579524 257717 6023839 18775483 8431507 1580597 4933076 2213508
5.48% 17.20% 7.65% 5.41% 16.85% 7.57% 5.40% 16.85% 7.56%
Total CpG mut: 521313 Total CpG mut: 29324595 Total CpG mut: 7706136
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
43396 43910 173451 2561516 2578414 9521382 673839 678659 2499906
8.32% 8.42% 33.27% 8.74% 8.79% 32.47% 8.74% 8.81% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
172705 43907 43944 9524194 2575025 2564064 2503229 676358 674145
33.13% 8.42% 8.43% 32.48% 8.78% 8.74% 32.48% 8.78% 8.75%
Chromosome considered: 15 Chromosome considered: 15 Chromosome considered: 15
Total mut: 3602395 Total mut: 119733534 Total mut: 31617881
#AC AG AT #AC AG AT #AC AG AT
251610 606895 218961 9053157 20176380 6467574 2390300 5329468 1708504
6.98% 16.85% 6.08% 7.56% 16.85% 5.40% 7.56% 16.86% 5.40%
#CA CG CT #CA CG CT #CA CG CT
126033 101950 493603 3997791 3966430 16149453 1056395 1048246 4264896
3.50% 2.83% 13.70% 3.34% 3.31% 13.49% 3.34% 3.32% 13.49%
#GA GC GT #GA GC GT #GA GC GT
494121 102382 125047 16150327 3978760 4009740 4263245 1049365 1057691
13.72% 2.84% 3.47% 13.49% 3.32% 3.35% 13.48% 3.32% 3.35%
#TA TC TG #TA TC TG #TA TC TG
218780 610525 252488 6485793 20219832 9078297 1711266 5342032 2396473
6.07% 16.95% 7.01% 5.42% 16.89% 7.58% 5.41% 16.90% 7.58%
Total CpG mut: 456863 Total CpG mut: 30947066 Total CpG mut: 8154852
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
42308 35225 150891 2703503 2721198 10048075 713085 718029 2645571
9.26% 7.71% 33.03% 8.74% 8.79% 32.47% 8.74% 8.80% 32.44%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
150376 35558 42505 10050245 2717735 2706310 2649084 715813 713270
32.91% 7.78% 9.30% 32.48% 8.78% 8.74% 32.48% 8.78% 8.75%
Chromosome considered: 16 Chromosome considered: 16 Chromosome considered: 16
Total mut: 2353352 Total mut: 125136983 Total mut: 33231571
#AC AG AT #AC AG AT #AC AG AT
177600 398557 137065 9473388 21114078 6767933 2514740 5607076 1797718
7.55% 16.94% 5.82% 7.57% 16.87% 5.41% 7.57% 16.87% 5.41%
#CA CG CT #CA CG CT #CA CG CT
78630 71906 308940 4171901 4139430 16852294 1109073 1100645 4476582
3.34% 3.06% 13.13% 3.33% 3.31% 13.47% 3.34% 3.31% 13.47%
#GA GC GT #GA GC GT #GA GC GT
308511 72022 77257 16851203 4151074 4183306 4474912 1101424 1110144
13.11% 3.06% 3.28% 13.47% 3.32% 3.34% 13.47% 3.31% 3.34%
#TA TC TG #TA TC TG #TA TC TG
138294 406902 177668 6784889 21150775 9496712 1800011 5618647 2520599
5.88% 17.29% 7.55% 5.42% 16.90% 7.59% 5.42% 16.91% 7.58%
Total CpG mut: 299738 Total CpG mut: 32000829 Total CpG mut: 8482190
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
27247 25178 97747 2795391 2813576 10390721 741673 746741 2752208
9.09% 8.40% 32.61% 8.74% 8.79% 32.47% 8.74% 8.80% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
97304 25473 26789 10392773 2810340 2798028 2755258 744478 741832
32.46% 8.50% 8.94% 32.48% 8.78% 8.74% 32.48% 8.78% 8.75%
Chromosome considered: 17 Chromosome considered: 17 Chromosome considered: 17
Total mut: 810302 Total mut: 126975149 Total mut: 33453618
#AC AG AT #AC AG AT #AC AG AT
63918 144738 44970 9606607 21410802 6862605 2530986 5643481 1809254
7.89% 17.86% 5.55% 7.57% 16.86% 5.40% 7.57% 16.87% 5.41%
#CA CG CT #CA CG CT #CA CG CT
26743 28059 96690 4237039 4204305 17116491 1116862 1108409 4508050
3.30% 3.46% 11.93% 3.34% 3.31% 13.48% 3.34% 3.31% 13.48%
#GA GC GT #GA GC GT #GA GC GT
97528 28131 26855 17114011 4215732 4248651 4505950 1109133 1117900
12.04% 3.47% 3.31% 13.48% 3.32% 3.35% 13.47% 3.32% 3.34%
#TA TC TG #TA TC TG #TA TC TG
44820 143941 63909 6879887 21448466 9630553 1811737 5654985 2536871
5.53% 17.76% 7.89% 5.42% 16.89% 7.58% 5.42% 16.90% 7.58%
Total CpG mut: 120720 Total CpG mut: 33291054 Total CpG mut: 8639922
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
10697 12446 37131 2908050 2927347 10809049 755619 760466 2803430
8.86% 10.31% 30.76% 8.74% 8.79% 32.47% 8.75% 8.80% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
37128 12336 10982 10811750 2923553 2911305 2806697 758234 755476
30.76% 10.22% 9.10% 32.48% 8.78% 8.75% 32.49% 8.78% 8.74%
Chromosome considered: 18 Chromosome considered: 18 Chromosome considered: 18
Total mut: 1666982 Total mut: 130762261 Total mut: 34542476
#AC AG AT #AC AG AT #AC AG AT
150802 316645 84028 9888940 22041003 7064896 2611564 5823536 1866974
9.05% 19.00% 5.04% 7.56% 16.86% 5.40% 7.56% 16.86% 5.40%
#CA CG CT #CA CG CT #CA CG CT
42765 53489 183247 4366519 4332932 17640127 1154018 1145458 4659132
2.57% 3.21% 10.99% 3.34% 3.31% 13.49% 3.34% 3.32% 13.49%
#GA GC GT #GA GC GT #GA GC GT
183580 54007 43143 17634290 4344280 4378006 4656848 1146433 1155416
11.01% 3.24% 2.59% 13.49% 3.32% 3.35% 13.48% 3.32% 3.34%
#TA TC TG #TA TC TG #TA TC TG
84650 318468 152158 7081459 22077579 9912230 1869670 5835674 2617753
5.08% 19.10% 9.13% 5.42% 16.88% 7.58% 5.41% 16.89% 7.58%
Total CpG mut: 202245 Total CpG mut: 34331911 Total CpG mut: 8950144
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
16753 20703 63830 2998984 3019166 11147270 782556 787716 2904528
8.28% 10.24% 31.56% 8.74% 8.79% 32.47% 8.74% 8.80% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
63895 20400 16664 11149358 3014758 3002375 2907257 785513 782574
31.59% 10.09% 8.24% 32.48% 8.78% 8.75% 32.48% 8.78% 8.74%
Chromosome considered: X Chromosome considered: X Chromosome considered: X
Total mut: 1823851 Total mut: 134936174 Total mut: 35226480
#AC AG AT #AC AG AT #AC AG AT
144756 315876 101715 10211562 22761833 7295313 2663718 5940795 1904163
7.94% 17.32% 5.58% 7.57% 16.87% 5.41% 7.56% 16.86% 5.41%
#CA CG CT #CA CG CT #CA CG CT
62374 57207 229083 4501134 4466416 18182810 1176371 1167698 4749353
3.42% 3.14% 12.56% 3.34% 3.31% 13.48% 3.34% 3.31% 13.48%
#GA GC GT #GA GC GT #GA GC GT
229993 57645 62706 18176996 4477904 4513045 4746693 1168642 1177699
12.61% 3.16% 3.44% 13.47% 3.32% 3.34% 13.47% 3.32% 3.34%
#TA TC TG #TA TC TG #TA TC TG
102627 314752 145117 7313110 22800195 10235856 1907220 5953455 2670673
5.63% 17.26% 7.96% 5.42% 16.90% 7.59% 5.41% 16.90% 7.58%
Total CpG mut: 206464 Total CpG mut: 35804987 Total CpG mut: 9218945
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
18801 17472 66953 3128098 3148439 11625359 805816 811512 2991776
9.11% 8.46% 32.43% 8.74% 8.79% 32.47% 8.74% 8.80% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
67030 17313 18895 11627995 3143938 3131158 2994840 808919 806082
32.47% 8.39% 9.15% 32.48% 8.78% 8.75% 32.49% 8.77% 8.74%